assume the LTR checks are done

## [1] 413
## 
##  we have 413  samples in common
##  and  5  samples in the experimental data that are not in metadata

0.0.1 NMR spectra post processing

0.0.2 Step 1 Spectra calibration

Lets check the alanine doublets as it is

Lets see after calibration

0.0.3 Step 2 Remove the regions of the spectra that are not of interest

0.0.4 Step 3 Baseline correction

0.0.5 Step 4 Normalization

1 Analysis

1.1 PCA

## 
##  who are those PC3 outliers and why?
##     sampleID projectName cohortName sampleMatrixType    tubeLabel sourceID
## 868 FIB00912      fibers         C1              URI fib380-u1-t2   fib380
## 869 FIB00917      fibers         C1              URI fib380-u1-t4   fib380
## 870 FIB00935      fibers         C1              URI fib380-u1-t6   fib380
## 871 FIB00944      fibers         C1              URI fib380-u1-t8   fib380
## 867 FIB00901      fibers         C1              URI fib380-u1-t0   fib380
##     sampleTimePoint          visit timePoint            type typeId
## 868           t2-u1 Clinic Visit 1        T2 Elephant Garlic     V1
## 869           t4-u1 Clinic Visit 1        T4 Elephant Garlic     V1
## 870           t6-u1 Clinic Visit 1        T6 Elephant Garlic     V1
## 871           t8-u1 Clinic Visit 1        T8 Elephant Garlic     V1
## 867           t0-u1 Clinic Visit 1        T0 Elephant Garlic     V1
##     sampleTimePoint         key bmi age    sex        DOB height Weight
## 868           t2-v1 fib380t2-v1  22  34 Female 1989-01-07  167.5   60.6
## 869           t4-v1 fib380t4-v1  22  34 Female 1989-01-07  167.5   60.6
## 870           t6-v1 fib380t6-v1  22  34 Female 1989-01-07  167.5   60.6
## 871           t8-v1 fib380t8-v1  22  34 Female 1989-01-07  167.5   60.6
## 867           t0-v1 fib380t0-v1  22  34 Female 1989-01-07  167.5   60.6
##     Screen Visit Date Screen Visit H2BT  food date Clinic Visit Date
## 868        2023-11-02                 6 2023-12-07        2023-12-07
## 869        2023-11-02                49 2023-12-07        2023-12-07
## 870        2023-11-02                27 2023-12-07        2023-12-07
## 871        2023-11-02                38 2023-12-07        2023-12-07
## 867        2023-11-02                 2 2023-12-07        2023-12-07
##     Clinic Visit H2BT Non standard Food Medication Activity
## 868                 2              <NA>       <NA>     <NA>
## 869                 2              <NA>       <NA>     <NA>
## 870                25              <NA>       <NA>     <NA>
## 871                49              <NA>       <NA>     <NA>
## 867                 5              <NA>       <NA>     <NA>
## 
##  PC3 outliers are from the same person: fib380 eating  Elephant Garlic collected from 5 different timepoints

## 
##  From the loadings, it seems that those outliers are from high glucose in urine
## 
##  Since this participant only participated in the Elephant Garlic study it may be wise to remove from the analysis

1.2 COMPASS

1.3 Visual Inspection using specOverlay

soutceID fib 380 (high glucose outlier) were omitted and only ploted at Timepoint T2, T4, T6, and T8

1.3.1 2,3-butanediol 1.125 ~ 1.150 –> Yacon

1.3.2 lactate 1.3 ~ 1.5 –> Apple at T2

1.3.3 s 1.92 –> Global Artichoke at T2? –> only two samples

1.3.4 s 2.045 –> Elephant Garlic peak at T4

1.3.5 s 3.1 –> Orange

1.3.6 s 3.3 –> Orange